HEADER IMMUNE SYSTEM 19-MAR-21 7M3Y TITLE STRUCTURE OF TIM-3 IN COMPLEX WITH 8-CHLORO-2-METHYL-9-(3- TITLE 2 MEHTYLPYRIDIN-4-YL)-[1,2,4]TRIAZOLO[1,5-C]QUINAZOLIN-5(6H)-ONE TITLE 3 (COMPOUND 22) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEPATITIS A VIRUS CELLULAR RECEPTOR 2; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: HAVCR-2,T-CELL IMMUNOGLOBULIN AND MUCIN DOMAIN-CONTAINING COMPND 5 PROTEIN 3,TIMD-3,T-CELL IMMUNOGLOBULIN MUCIN RECEPTOR 3,TIM-3,T-CELL COMPND 6 MEMBRANE PROTEIN 3; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HAVCR2, TIM3, TIMD3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS IGV, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR T.A.RIETZ REVDAT 3 18-OCT-23 7M3Y 1 REMARK REVDAT 2 27-OCT-21 7M3Y 1 JRNL REVDAT 1 13-OCT-21 7M3Y 0 JRNL AUTH T.A.RIETZ,K.B.TEUSCHER,J.J.MILLS,R.D.GOGLIOTTI,L.T.LEPOVITZ, JRNL AUTH 2 W.R.SCAGGS,K.YOSHIDA,K.LUONG,T.LEE,S.W.FESIK JRNL TITL FRAGMENT-BASED DISCOVERY OF SMALL MOLECULES BOUND TO T-CELL JRNL TITL 2 IMMUNOGLOBULIN AND MUCIN DOMAIN-CONTAINING MOLECULE 3 JRNL TITL 3 (TIM-3). JRNL REF J.MED.CHEM. V. 64 14757 2021 JRNL REFN ISSN 0022-2623 JRNL PMID 34597046 JRNL DOI 10.1021/ACS.JMEDCHEM.1C01336 REMARK 2 REMARK 2 RESOLUTION. 1.69 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 12384 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.440 REMARK 3 FREE R VALUE TEST SET COUNT : 674 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 26.8500 - 2.8900 1.00 2440 139 0.1739 0.1876 REMARK 3 2 2.8900 - 2.3000 1.00 2361 121 0.2040 0.2696 REMARK 3 3 2.3000 - 2.0100 1.00 2302 162 0.1812 0.2237 REMARK 3 4 2.0100 - 1.8200 1.00 2312 130 0.1858 0.1917 REMARK 3 5 1.8200 - 1.6900 0.99 2295 122 0.2214 0.2451 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.910 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.52 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.88 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7M3Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1000255602. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUL-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12404 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.690 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : 0.76300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.1 REMARK 200 STARTING MODEL: 5F71 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.8 M SODIUM TARTRATE DIBASIC REMARK 280 DIHYDRATE, 0.1 M HEPES PH 6.8-8.2, AND 10 MM CACL2, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.84850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 26.84850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 23.47900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 42.67150 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 23.47900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 42.67150 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 26.84850 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 23.47900 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 42.67150 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 26.84850 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 23.47900 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 42.67150 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 381 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 383 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PHE B 40 -122.10 51.49 REMARK 500 CYS B 42 39.86 -144.08 REMARK 500 ASP B 50 -153.73 -120.07 REMARK 500 ARG B 60 -10.44 90.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 202 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE B 93 O REMARK 620 2 GLY B 95 O 99.5 REMARK 620 3 ASN B 98 OD1 84.7 78.9 REMARK 620 4 ASP B 99 OD1 93.9 166.6 102.4 REMARK 620 5 HOH B 387 O 85.9 92.6 166.1 88.5 REMARK 620 N 1 2 3 4 DBREF 7M3Y B 1 109 UNP Q8TDQ0 HAVR2_HUMAN 22 130 SEQRES 1 B 109 SER GLU VAL GLU TYR ARG ALA GLU VAL GLY GLN ASN ALA SEQRES 2 B 109 TYR LEU PRO CYS PHE TYR THR PRO ALA ALA PRO GLY ASN SEQRES 3 B 109 LEU VAL PRO VAL CYS TRP GLY LYS GLY ALA CYS PRO VAL SEQRES 4 B 109 PHE GLU CYS GLY ASN VAL VAL LEU ARG THR ASP GLU ARG SEQRES 5 B 109 ASP VAL ASN TYR TRP THR SER ARG TYR TRP LEU ASN GLY SEQRES 6 B 109 ASP PHE ARG LYS GLY ASP VAL SER LEU THR ILE GLU ASN SEQRES 7 B 109 VAL THR LEU ALA ASP SER GLY ILE TYR CYS CYS ARG ILE SEQRES 8 B 109 GLN ILE PRO GLY ILE MET ASN ASP GLU LYS PHE ASN LEU SEQRES 9 B 109 LYS LEU VAL ILE LYS HET YQ7 B 201 23 HET CA B 202 1 HETNAM YQ7 (4R,10AP)-8-CHLORO-2-METHYL-9-(3-METHYLPYRIDIN-4-YL)[1, HETNAM 2 YQ7 2,4]TRIAZOLO[1,5-C]QUINAZOLIN-5(6H)-ONE HETNAM CA CALCIUM ION FORMUL 2 YQ7 C16 H12 CL N5 O FORMUL 3 CA CA 2+ FORMUL 4 HOH *111(H2 O) HELIX 1 AA1 ASP B 66 GLY B 70 5 5 HELIX 2 AA2 THR B 80 SER B 84 5 5 SHEET 1 AA1 6 TYR B 5 GLU B 8 0 SHEET 2 AA1 6 GLU B 100 LYS B 109 1 O VAL B 107 N TYR B 5 SHEET 3 AA1 6 GLY B 85 ILE B 91 -1 N ILE B 91 O GLU B 100 SHEET 4 AA1 6 VAL B 30 LYS B 34 -1 N CYS B 31 O ARG B 90 SHEET 5 AA1 6 ASN B 44 THR B 49 -1 O LEU B 47 N TRP B 32 SHEET 6 AA1 6 VAL B 54 TRP B 57 -1 O TYR B 56 N ARG B 48 SHEET 1 AA2 3 ALA B 13 LEU B 15 0 SHEET 2 AA2 3 LEU B 74 ILE B 76 -1 O LEU B 74 N LEU B 15 SHEET 3 AA2 3 TYR B 61 TRP B 62 -1 N TRP B 62 O THR B 75 SSBOND 1 CYS B 17 CYS B 89 1555 1555 2.03 SSBOND 2 CYS B 31 CYS B 42 1555 1555 2.04 SSBOND 3 CYS B 37 CYS B 88 1555 1555 2.03 LINK O ILE B 93 CA CA B 202 1555 1555 2.28 LINK O GLY B 95 CA CA B 202 1555 1555 2.39 LINK OD1 ASN B 98 CA CA B 202 1555 1555 2.32 LINK OD1 ASP B 99 CA CA B 202 1555 1555 2.35 LINK CA CA B 202 O HOH B 387 1555 1555 2.42 CRYST1 46.958 85.343 53.697 90.00 90.00 90.00 C 2 2 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.021296 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011717 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018623 0.00000